Job ID = 9041298 sra ファイルのダウンロード中... Completed: 237255K bytes transferred in 4 seconds (418922K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 7663 0 7663 0 0 1025 0 --:--:-- 0:00:07 --:--:-- 8639 100 30318 0 30318 0 0 3580 0 --:--:-- 0:00:08 --:--:-- 16100 100 46800 0 46800 0 0 5196 0 --:--:-- 0:00:09 --:--:-- 19338 sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... 2017-06-04T15:40:18 fastq-dump.2.3.2 err: file descriptor not found while accessing file within file system module - error with curl open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_004354.3' 2017-06-04T15:40:19 fastq-dump.2.3.2 err: name not found while resolving tree within virtual file system module - failed /home/okishinya/chipatlas/results/dm3/SRX1167500/SRR2192589.sra Written 0 spots total ============================================================= An error occurred during processing. A report was generated into the file '/home/okishinya/ncbi_error_report.xml'. If the problem persists, you may consider sending the file to 'sra@ncbi.nlm.nih.gov' for assistance. ============================================================= rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:14 12634368 reads; of these: 12634368 (100.00%) were unpaired; of these: 144983 (1.15%) aligned 0 times 12308279 (97.42%) aligned exactly 1 time 181106 (1.43%) aligned >1 times 98.85% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 5484967 / 12489385 = 0.4392 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 05 Jun 2017 00:43:12: # Command line: callpeak -t SRX1167500.bam -f BAM -g dm -n SRX1167500.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1167500.10 # format = BAM # ChIP-seq file = ['SRX1167500.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Mon, 05 Jun 2017 00:43:12: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:43:12: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:43:12: # Command line: callpeak -t SRX1167500.bam -f BAM -g dm -n SRX1167500.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1167500.20 # format = BAM # ChIP-seq file = ['SRX1167500.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Mon, 05 Jun 2017 00:43:12: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:43:12: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:43:12: # Command line: callpeak -t SRX1167500.bam -f BAM -g dm -n SRX1167500.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1167500.05 # format = BAM # ChIP-seq file = ['SRX1167500.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Mon, 05 Jun 2017 00:43:12: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:43:12: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:43:18: 1000000 INFO @ Mon, 05 Jun 2017 00:43:18: 1000000 INFO @ Mon, 05 Jun 2017 00:43:18: 1000000 INFO @ Mon, 05 Jun 2017 00:43:24: 2000000 INFO @ Mon, 05 Jun 2017 00:43:25: 2000000 INFO @ Mon, 05 Jun 2017 00:43:25: 2000000 INFO @ Mon, 05 Jun 2017 00:43:30: 3000000 INFO @ Mon, 05 Jun 2017 00:43:31: 3000000 INFO @ Mon, 05 Jun 2017 00:43:31: 3000000 INFO @ Mon, 05 Jun 2017 00:43:36: 4000000 INFO @ Mon, 05 Jun 2017 00:43:38: 4000000 INFO @ Mon, 05 Jun 2017 00:43:38: 4000000 INFO @ Mon, 05 Jun 2017 00:43:42: 5000000 INFO @ Mon, 05 Jun 2017 00:43:44: 5000000 INFO @ Mon, 05 Jun 2017 00:43:44: 5000000 INFO @ Mon, 05 Jun 2017 00:43:48: 6000000 INFO @ Mon, 05 Jun 2017 00:43:50: 6000000 INFO @ Mon, 05 Jun 2017 00:43:50: 6000000 INFO @ Mon, 05 Jun 2017 00:43:54: 7000000 INFO @ Mon, 05 Jun 2017 00:43:54: #1 tag size is determined as 37 bps INFO @ Mon, 05 Jun 2017 00:43:54: #1 tag size = 37 INFO @ Mon, 05 Jun 2017 00:43:54: #1 total tags in treatment: 7004418 INFO @ Mon, 05 Jun 2017 00:43:54: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:43:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:43:55: #1 tags after filtering in treatment: 7002999 INFO @ Mon, 05 Jun 2017 00:43:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:43:55: #1 finished! INFO @ Mon, 05 Jun 2017 00:43:55: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:43:57: 7000000 INFO @ Mon, 05 Jun 2017 00:43:57: 7000000 INFO @ Mon, 05 Jun 2017 00:43:57: #2 number of paired peaks: 126 WARNING @ Mon, 05 Jun 2017 00:43:57: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Mon, 05 Jun 2017 00:43:57: start model_add_line... INFO @ Mon, 05 Jun 2017 00:43:57: #1 tag size is determined as 37 bps INFO @ Mon, 05 Jun 2017 00:43:57: #1 tag size = 37 INFO @ Mon, 05 Jun 2017 00:43:57: #1 total tags in treatment: 7004418 INFO @ Mon, 05 Jun 2017 00:43:57: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:43:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:43:57: #1 tag size is determined as 37 bps INFO @ Mon, 05 Jun 2017 00:43:57: #1 tag size = 37 INFO @ Mon, 05 Jun 2017 00:43:57: #1 total tags in treatment: 7004418 INFO @ Mon, 05 Jun 2017 00:43:57: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:43:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:43:58: #1 tags after filtering in treatment: 7002999 INFO @ Mon, 05 Jun 2017 00:43:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:43:58: #1 finished! INFO @ Mon, 05 Jun 2017 00:43:58: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:43:58: start X-correlation... INFO @ Mon, 05 Jun 2017 00:43:58: end of X-cor INFO @ Mon, 05 Jun 2017 00:43:58: #2 finished! INFO @ Mon, 05 Jun 2017 00:43:58: #2 predicted fragment length is 156 bps INFO @ Mon, 05 Jun 2017 00:43:58: #2 alternative fragment length(s) may be 156,185,596,598 bps INFO @ Mon, 05 Jun 2017 00:43:58: #2.2 Generate R script for model : SRX1167500.20_model.r INFO @ Mon, 05 Jun 2017 00:43:58: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:43:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:43:58: #1 tags after filtering in treatment: 7002999 INFO @ Mon, 05 Jun 2017 00:43:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:43:58: #1 finished! INFO @ Mon, 05 Jun 2017 00:43:58: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:43:59: #2 number of paired peaks: 126 WARNING @ Mon, 05 Jun 2017 00:43:59: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Mon, 05 Jun 2017 00:43:59: start model_add_line... INFO @ Mon, 05 Jun 2017 00:44:00: #2 number of paired peaks: 126 WARNING @ Mon, 05 Jun 2017 00:44:00: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Mon, 05 Jun 2017 00:44:00: start model_add_line... INFO @ Mon, 05 Jun 2017 00:44:01: start X-correlation... INFO @ Mon, 05 Jun 2017 00:44:01: end of X-cor INFO @ Mon, 05 Jun 2017 00:44:01: #2 finished! INFO @ Mon, 05 Jun 2017 00:44:01: #2 predicted fragment length is 156 bps INFO @ Mon, 05 Jun 2017 00:44:01: #2 alternative fragment length(s) may be 156,185,596,598 bps INFO @ Mon, 05 Jun 2017 00:44:01: #2.2 Generate R script for model : SRX1167500.05_model.r INFO @ Mon, 05 Jun 2017 00:44:01: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:44:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:44:01: start X-correlation... INFO @ Mon, 05 Jun 2017 00:44:01: end of X-cor INFO @ Mon, 05 Jun 2017 00:44:01: #2 finished! INFO @ Mon, 05 Jun 2017 00:44:01: #2 predicted fragment length is 156 bps INFO @ Mon, 05 Jun 2017 00:44:01: #2 alternative fragment length(s) may be 156,185,596,598 bps INFO @ Mon, 05 Jun 2017 00:44:01: #2.2 Generate R script for model : SRX1167500.10_model.r INFO @ Mon, 05 Jun 2017 00:44:01: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:44:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:44:37: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:44:38: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:44:40: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:45:04: #4 Write output xls file... SRX1167500.05_peaks.xls INFO @ Mon, 05 Jun 2017 00:45:04: #4 Write peak in narrowPeak format file... SRX1167500.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:45:04: #4 Write summits bed file... SRX1167500.05_summits.bed INFO @ Mon, 05 Jun 2017 00:45:04: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (288 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:45:05: #4 Write output xls file... SRX1167500.20_peaks.xls INFO @ Mon, 05 Jun 2017 00:45:05: #4 Write peak in narrowPeak format file... SRX1167500.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:45:05: #4 Write summits bed file... SRX1167500.20_summits.bed INFO @ Mon, 05 Jun 2017 00:45:05: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (22 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:45:08: #4 Write output xls file... SRX1167500.10_peaks.xls INFO @ Mon, 05 Jun 2017 00:45:08: #4 Write peak in narrowPeak format file... SRX1167500.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:45:08: #4 Write summits bed file... SRX1167500.10_summits.bed INFO @ Mon, 05 Jun 2017 00:45:08: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (98 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。